---
title: ggVennDiagram 的新生
author: Chun-Hui Gao
date: '2021-05-08'
categories:
  - ggplot
tags:
  - ggplot
  - ggVennDiagram
slug: ggvenndiagram-reborn
---

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<p><code>ggVennDiagram</code> 是一个用于绘制 Venn 图的 R 语言软件包。最初，我只是在需要画 Venn
图的时候，发现没有一件趁手的工具，而最终不得不写了一个给自己用的工具。随后，
抱着试一试的态度发布到了 GitHub 和 CRAN 上面。结果引起了用户持续的关注和好评，
截止今日已经获得了超过 100 个小星星。</p>
<p><img src="/post/2021-5-8-ggVennDiagram-reborn_files/figure-html/unnamed-chunk-1-1.png" width="672" /></p>
<p>在 CRAN 上面也已经被累计下载了 2 万多次了。</p>
<p><a href="https://cran.r-project.org/package=ggVennDiagram"><img src="http://cranlogs.r-pkg.org/badges/grand-total/ggVennDiagram?color=green" /></a>
<a href="https://cran.r-project.org/package=ggVennDiagram"><img src="https://www.r-pkg.org/badges/version/ggVennDiagram?color=green" /></a></p>
<p>考虑到原来的设计和代码是十分粗糙的，所以我在 1.0 版本的时候，完全重构了 <code>ggVennDiagram</code><a href="#fn1" class="footnote-ref" id="fnref1"><sup>1</sup></a>。</p>
<p>为此，系统调研了 R 环境中可用的 Venn 图绘制工具，博取众家之长，并增强了自己原有的特色和优势。
重生后的 <code>ggVennDiagram</code> 用起来更加方便，功能也更加强大，同时以后的扩展性也会非常好。</p>
<p>下面是一些使用的示例：</p>
<p>先生成一个示例数据：</p>
<pre class="r"><code>genes &lt;- paste0(&quot;gene&quot;,1:1000)
set.seed(20210502)
gene_list &lt;- list(A = sample(genes,100),
                  B = sample(genes,200),
                  C = sample(genes,300),
                  D = sample(genes,200))

library(ggVennDiagram)</code></pre>
<div id="设置集合标签的内容颜色和大小" class="section level2">
<h2>设置集合标签的内容，颜色和大小</h2>
<p>标签图层在最上面，不会被填充遮盖。但是如果是非常长的标签，可能会显示不完整。
此时只需要应用一个 <code>ggplot2</code> 函数即可。</p>
<pre class="r"><code>ggVennDiagram(gene_list, 
              category.names = c(&quot;a very long name&quot;,&quot;short name&quot;,&quot;name&quot;,&quot;another name&quot;),
              set_color = c(&quot;red1&quot;,&quot;red2&quot;,&quot;red3&quot;,&quot;red4&quot;),
              set_size = 6) +
  scale_x_continuous(expand = expansion(mult = .2))</code></pre>
<p><img src="/post/2021-5-8-ggVennDiagram-reborn_files/figure-html/unnamed-chunk-3-1.png" width="672" /></p>
</div>
<div id="显示区域中的成员" class="section level2">
<h2>显示区域中的成员</h2>
<p>我们使用 <code>plotly</code> 对区域成员进行了可视化，现在鼠标悬停即可以查看区域成员。
同时，也支持将成员打印出来。</p>
<pre class="r"><code>ggVennDiagram(gene_list, show_intersect = TRUE)</code></pre>
<pre><code>## Warning: Ignoring unknown aesthetics: text</code></pre>
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</div>
<div id="设定区域标签的内容颜色和大小" class="section level2">
<h2>设定区域标签的内容、颜色和大小</h2>
<pre class="r"><code>ggVennDiagram(gene_list, label = &quot;count&quot;, label_color = &quot;blue&quot;, label_size = 4)</code></pre>
<p><img src="/post/2021-5-8-ggVennDiagram-reborn_files/figure-html/unnamed-chunk-5-1.png" width="672" /></p>
<pre class="r"><code>ggVennDiagram(gene_list, label = &quot;both&quot;, label_percent_digit = 1, label_size = 3)</code></pre>
<p><img src="/post/2021-5-8-ggVennDiagram-reborn_files/figure-html/unnamed-chunk-6-1.png" width="672" /></p>
</div>
<div id="设定椭圆的边" class="section level2">
<h2>设定椭圆的边</h2>
<pre class="r"><code>ggVennDiagram(gene_list, edge_lty = &quot;dashed&quot;, edge_size = 1)</code></pre>
<p><img src="/post/2021-5-8-ggVennDiagram-reborn_files/figure-html/unnamed-chunk-7-1.png" width="672" /></p>
</div>
<div id="换一个配色" class="section level2">
<h2>换一个配色</h2>
<p>填充色映射到不同的区域中。</p>
<pre class="r"><code>ggVennDiagram(gene_list) + scale_fill_distiller(palette = &quot;RdBu&quot;)</code></pre>
<p><img src="/post/2021-5-8-ggVennDiagram-reborn_files/figure-html/unnamed-chunk-8-1.png" width="672" /></p>
<p>线条颜色映射到不同的集合上。</p>
<pre class="r"><code>ggVennDiagram(gene_list) + scale_color_brewer(palette = &quot;Set1&quot;)</code></pre>
<p><img src="/post/2021-5-8-ggVennDiagram-reborn_files/figure-html/unnamed-chunk-9-1.png" width="672" /></p>
</div>
<div id="更多维度的-venn-图" class="section level2">
<h2>更多维度的 Venn 图</h2>
<p>通过导入另一个 R 包 <code>venn</code> 中的数据集，将 5-7 维度的 Venn 图画法移植了过来。</p>
<pre class="r"><code>genes &lt;- paste0(&quot;gene&quot;,1:1000)
set.seed(20210507)
x &lt;- list(A = sample(genes,100),
          B = sample(genes,150),
          C = sample(genes,200),
          D = sample(genes,250),
          E = sample(genes,300),
          F = sample(genes,350),
          G = sample(genes,400))</code></pre>
<p>由于是用的不规则多边形，所以这些 Venn 图可能辨别起来会比较费劲，但是乍看上去还是蛮漂亮的。</p>
<pre class="r"><code>ggVennDiagram(x, label = &quot;none&quot;, edge_size = 2) + scale_fill_distiller(palette = &quot;RdBu&quot;)</code></pre>
<p><img src="/post/2021-5-8-ggVennDiagram-reborn_files/figure-html/unnamed-chunk-11-1.png" width="672" /></p>
<pre class="r"><code>ggVennDiagram(x[1:6], label = &quot;none&quot;, edge_size = 2) + scale_fill_distiller(palette = &quot;RdBu&quot;)</code></pre>
<p><img src="/post/2021-5-8-ggVennDiagram-reborn_files/figure-html/unnamed-chunk-11-2.png" width="672" /></p>
<pre class="r"><code>ggVennDiagram(x[1:5], label = &quot;none&quot;, edge_size = 2) + scale_fill_distiller(palette = &quot;RdBu&quot;)</code></pre>
<p><img src="/post/2021-5-8-ggVennDiagram-reborn_files/figure-html/unnamed-chunk-11-3.png" width="672" /></p>
</div>
<div id="自由定制" class="section level2">
<h2>自由定制</h2>
<p><code>ggVennDiagram</code> 将 Venn 图分为了 3 个部分，集合的标签，集合的边缘，集合的交叉，
分别称为 <code>setLabel</code>，<code>setEdge</code> 和 <code>region</code>。我们所做的主要工作是将繁琐的集合间计算
过程包装了起来（包括多边形区域的坐标及其对应成员的统计），并将计算的结果返回，
然后使用 <code>ggplot</code> 画图。</p>
<pre class="r"><code>venn &lt;- Venn(gene_list)
data &lt;- process_data(venn)
ggplot() +
  # 1. region count layer
  geom_sf(aes(fill = count), data = venn_region(data)) +
  # 2. set edge layer
  geom_sf(aes(color = id), data = venn_setedge(data), show.legend = FALSE) +
  # 3. set label layer
  geom_sf_text(aes(label = name), data = venn_setlabel(data)) +
  # 4. region label layer
  geom_sf_label(aes(label = count), data = venn_region(data)) +
  theme_void()</code></pre>
<p><img src="/post/2021-5-8-ggVennDiagram-reborn_files/figure-html/unnamed-chunk-12-1.png" width="672" /></p>
<p>对于熟悉 <code>ggplot</code> 作图的用户来说，他完全可以任意定制作图的格式。</p>
<pre class="r"><code>ggplot() +
  # change mapping of color filling
  geom_sf(aes(fill = id), data = venn_region(data), show.legend = FALSE) +  
  # adjust edge size and color
  geom_sf(color=&quot;grey&quot;, size = 3, data = venn_setedge(data), show.legend = FALSE) +  
  # show set label in bold
  geom_sf_text(aes(label = name), fontface = &quot;bold&quot;, data = venn_setlabel(data)) +  
  # add a alternative region name
  geom_sf_label(aes(label = name), data = venn_region(data), alpha = 0.5) +  
  theme_void()</code></pre>
<p><img src="/post/2021-5-8-ggVennDiagram-reborn_files/figure-html/unnamed-chunk-13-1.png" width="672" /></p>
<p>新的 <code>ggVennDiagram</code> 更好用，更优雅。每一个绘制 Venn 图的朋友可能都会用得上。</p>
</div>
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